A goal of several projects was to determine the sequence-structure-function relationship of proteins with internal tandem repeats. In particular, sequence profiles were made to search sequence databases for arrays of tandem repeats in proteins of cell cycle regulation. Based on this analysis, toroidal alpha-helical models were suggested for the largest protein subunits Rpn1 and Rpn2 of 26S proteasome. Furthermore, it was proposed that Rpn1 and Rpn2 toroids are aligned along the common axial pores of the ATPase hexamer and form an antechamber of the 26S proteasome. It was also suggested that the function of this antechamber is to aid the ATPases in the unfolding of protein substrates prior to proteolysis. This result provides insight into the molecular mechanism of cell cycle regulation. In other work, we assessed the ability to model proteins with leucine-rich repeats (LRR) in light of the latest structural information by comparing models with the recently determined crystal structures. The comparison suggests that the general architecture, curvature, "interior/exterior" orientations of side chains, and backbone conformation of the LRR structures can be predicted correctly. The reliability of the LRR protein modeling suggests that it would be informative to apply similar modeling approaches to other classes of solenoid proteins. One of the projects deals with the structural arrangement of human cell envelopes and cornified epithelial cells of skin. The majority of the cell envelope proteins have sequence repeats. Possible three-dimensional structures of known proteins of the human cell envelope and their interactions with each other were analyzed. A mode of interaction between involucrin and small proline-rich proteins of the skin was suggested. Several projects involving the molecular modeling of globular proteins and the docking of their substrates were performed. For example, a red fluorescence protein was modeled in order to understand molecular processes occurring in "fluorescent timers," proteins that change color with time. An ongoing project concerns molecular docking of peptide substrates in the active site of the transglutaminase enzyme. Based on this docking, a specificity of the substrate binding is suggested. This will improve our understanding of the regulation of cross-linking of cell envelope proteins by this enzyme. In another project, the three-dimensional structure of the C-terminal part of atypical transcription factor Prospero was predicted and modeled. The relation between the model and known experimental data on its nuclear transport was analyzed. Finally, modeling of the complex between GalR repressor and HU protein allowed us to suggest several sites of mutations.